Recommendations for the description of protein sequence variants (v2.0)


Last modified August 17, 2011 - v2.0

Since references to WWW-sites are not yet acknowledged as citations, please mention den Dunnen JT and Antonarakis SE (2000). Hum.Mutat. 15:7-12 when referring to these pages.


Contents


Protein level

(suggestions extending the published recommendations in italics)


Protein designations describe a sequence variant at amino acid level. Protein level variants will rarely be experimentally determined, i.e. using amino acid sequencing. In some cases indirect evidence might come from from sizing (Western blot analysis) or localisation (immuno-histochemical staining). In most cases protein descriptions will be deduced, predicted from the changes detected on DNA and/or RNA level.

Sequence changes at protein level are described like those at the DNA level with the following modifications / additions;


Silent changes

Description of so called "silent" changes in the format p.(Leu54Leu) (or p.(L54L)) should not be used; descriptions should be given at DNA level (see Discussion).


Substitutions

Substitutions have the format p.Trp26Cys and do not use the ">"-character (indicating "changes to") used on DNA- and RNA level.


Deletions

Deletions are described using "del" after an indication of the first and last amino acid(s) deleted separated by a "_" (underscore).

NOTE: for all descriptions the most 3' position possible is arbitrarily assigned to have been changed


Duplications

Duplications are described using "dup" after an indication of the first and last amino acid(s) duplicated separated by a "_" (underscore).

NOTE: for all descriptions the most 3' position possible is arbitrarily assigned to have been changed


Insertions

Insertions are described using "ins" after an indication of the amino acids flanking the insertion site, separated by a "_" (underscore) and followed by a description of the amino acid(s) inserted. Duplicating insertions should be described as duplications (see Discussion), not as insertion. Since for large insertions the amino acids can be derived from the DNA and/or RNA descriptions they need not to be described exactly but the total number may be given (like "ins17").


Variability of short sequence repeats

Variability of short sequence repeats are described as p.Gln6(3_6); the description indicates that a stretch of Glutamines (Gln, Q) is present, starting at amino acid position 6 (e.g. in MKMGHQQQCC), which is found with a variable length from 3 to 6 in the population

NOTE: the underscore is used to indicate the range (3 to 6 times).


Insertion-deletions (indels)

Insertion-deletions (indels) are described using "delins" as a deletion followed by an insertion after an indication of the amino acid(s) flanking the site of the insertion/deletion separated by a "_" (underscore, see Discussion).


Frame shifts

Frame shifting variants are described using "fs" after the first amino acid affected by the change. Descriptions either use a short ("fs") or long ("fs*#") description. The description of frame shifts does not include the deletion at protein level from the site of the frame shift to the natural end of the protein (stop codon). For frame shifting insertions the inserted amino acid residues are not described, only the total length of the new shifted frame is given (i.e. including the inserted amino acids).
NOTE: typing error in den "Dunnen & Antonarakis (2000)". The suggestion to use ">" to indicate "delins" in frame shift descriptions has been retracted.

NOTE: the changes observed should be described on protein level and not try to incorporate any knowledge regarding the change at DNA-level (see Recommendation). Thus, p.His150Hisfs*10 is not correct, but p.Gln151Thrfs*9 is.


More changes in one individual

Two or more changes in one individual are described by combining the changes, per allele (chromosome) between brackets ("[]").


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